The Circulation of Type F Clostridium perfringens among Humans, Sewage, and Ruditapes philippinarum (Asari Clams)

6-plex Crystal Digital PCR® for comprehensive surveillance of respiratory and foodborne bacterial pathogens in wastewater

Bacterial wastewater surveillance (WS) is less explored area compared to viral WS despite high burden of bacterial respiratory and gastrointestinal infections worldwide. This study established a 6-plex Crystal Digital PCR® (cdPCR) system, to comprehensively monitor an acute respiratory pathogen - Group A Streptococcus (GAS) pyogenes, foodborne disease (FBD) pathogens - Clostridium perfringens, Salmonella spp., Campylobacter jejuni, and Campylobacter coli, and an indicator bacterium, Escherichia coli in wastewater. Fifty-two grab influent samples collected weekly from a wastewater treatment plant in Yamanashi Prefecture, Japan, between June 2023 and May 2024 were centrifuged, followed by DNA extraction and cdPCR. cdPCR was performed using the naica® system (Stilla Technologies). The 6-plex cdPCR assays showed strong performance. Among the 52 samples, 100 % of samples were positive for C. perfringens, 98 % for Salmonella spp., 56 % for C. jejuni, 25 % for C. coli, and 63 % for S. pyogenes, with concentrations ranging between 4.2 ± 0.3 to 7.5 ± 0.2 log10 copies/L. The concentration of C. perfringens was significantly higher than that of other pathogens (p < 0.05), indicating its dominance. Salmonella spp. had high detection rate, implying increased Salmonella infection in the population. Seasonal variation was not observed in any of FBD pathogens, except for the detection rate of C. coli. S. pyogenes concentrations were significantly higher in spring than in other seasons, agreeing with the trend of GAS pharyngitis cases in the catchment. In conclusion, the 6-plex cdPCR system is a valuable tool for comprehensive WS, offering significant implications for public health monitoring.

Investigation of the presence and persistence of bacteria in seawater and oysters from an aquaculture farm in Rehoboth Bay, Delaware

The filter-feeding nature of oysters, anthropogenic activities, and increasing agriculture in Delaware compromise the microbial safety of Eastern oysters from local aquaculture farms. From July to October 2023, we evaluated the presence and persistence of eight bacteria in seawater and oysters produced from off-bottom and bottom cultures at Sally Cove, an aquaculture farm within Rehoboth Bay in Delaware. A control site within Sally Cove, which was without oyster cultures, was also included in the study. Seawater temperature, salinity, pH, and dissolved oxygen were measured in situ during sampling. Molecular confirmation with PCR and qPCR showed that Vibrio parahaemolyticus, Shiga-toxin-producing Escherichia coli, Salmonella enterica, Staphylococcus aureus, Pseudomonas aeruginosa, and Clostridium spp. were present and persisted in seawater and oyster samples from both cultures at Sally Cove and in off-bottom and bottom seawater samples from the control site throughout the study. Shigella spp. and Listeria monocytogenes were consistently found in seawater and oyster samples from July to September. However, Shigella spp. was only detected in samples from the bottom cultures, whereas L. monocytogenes was undetectable in all samples from both cultures in October. The observed temperature, salinity, pH, and dissolved oxygen levels across the study period were in the range of 15.30-29.67°C, 29.33-31.87 ppt, 7.25-7.95, and 3.79-8.10 mg/L, respectively, and comparable with the conditions suitable for the growth and survival of these bacteria. These findings suggest that consuming raw oysters from Sally Cove poses contamination risks from several bacteria, especially in the summer months.IMPORTANCEAlthough studies have evaluated bacterial contamination in seawater and oysters within the Delaware Inland Bays and nearby areas, the focus has primarily been on Vibrio species. However, other bacteria have been found in seawater and seafood at various locations and could potentially occur in oysters produced from aquaculture farms within the Delaware Inland Bays. Sally Cove is an oyster aquaculture farm that produces Eastern oysters (Crassostrea virginica) for consumption in Delaware using both off-bottom and bottom culturing methods. The risk of bacterial contamination from consuming raw oysters from this farm is unknown. This paper shows the presence and persistence of several bacteria, including those associated with waste, in seawater and oysters at the farm. The findings can inform consumers about the contamination risks from consuming raw oysters produced at the farm.

Establishment and application of a rapid visual detection method for Clostridium perfringens in chicken products based on helical loop-mediated isothermal amplification (HAMP)

Clostridium perfringens is a significant foodborne pathogen in chicken products. Rapid on-site detection of C. perfringens is crucial for mitigating the incidence of foodborne illnesses by enabling the prompt identification and recall of contaminated food products. A rapid and visual detection method for C. perfringens in chicken products was developed using helical loop-mediated isothermal amplification (HAMP) technology combined with SYBR Green I fluorescent staining. The reaction temperature, time, and reagent concentrations of HAMP technique were optimized firstly. HAMP displayed high specificity, effectively distinguishing C. perfringens from 18 other common pathogens in chicken products. HAMP also exhibited higher sensitivity (78 fg/µL) compared to endpoint PCR and real-time quantitative PCR (qPCR). The detection limit of HAMP for non-enriched samples was 6.8 × 102 CFU/g, which improved to 68 and 6.8 CFU/g after 5 and 10 h of enrichment, respectively. The detection limit of HAMP was lower by 2 and 1 orders of magnitude compared to endpoint PCR and qPCR under the same conditions. On-site testing of commercially available ready-to-eat chicken products showed that HAMP had the same results as traditional culture methods, indicating the significant potential of HAMP for on-site detection of C. perfringens. This method offered a rapid, accurate, and visual means of detecting C. perfringens in chicken products, making it well-suited for on-site testing. This research represented the first use of the HAMP method for detecting C. perfringens.

The biology and pathogenicity of Clostridium perfringens type F: a common human enteropathogen with a new(ish) name

SUMMARYIn the 2018-revised Clostridium perfringens typing classification system, isolates carrying the enterotoxin (cpe) and alpha toxin genes but no other typing toxin genes are now designated as type F. Type F isolates cause food poisoning and nonfoodborne human gastrointestinal (GI) diseases, which most commonly involve type F isolates carrying, respectivefooly, a chromosomal or plasmid-borne cpe gene. Compared to spores of other C. perfringens isolates, spores of type F chromosomal cpe isolates often exhibit greater resistance to food environment stresses, likely facilitating their survival in improperly prepared or stored foods. Multiple factors contribute to this spore resistance phenotype, including the production of a variant small acid-soluble protein-4. The pathogenicity of type F isolates involves sporulation-dependent C. perfringens enterotoxin (CPE) production. C. perfringens sporulation is initiated by orphan histidine kinases and sporulation-associated sigma factors that drive cpe transcription. CPE-induced cytotoxicity starts when CPE binds to claudin receptors to form a small complex (which also includes nonreceptor claudins). Approximately six small complexes oligomerize on the host cell plasma membrane surface to form a prepore. CPE molecules in that prepore apparently extend β-hairpin loops to form a β-barrel pore, allowing a Ca2+ influx that activates calpain. With low-dose CPE treatment, caspase-3-dependent apoptosis develops, while high-CPE dose treatment induces necroptosis. Those effects cause histologic damage along with fluid and electrolyte losses from the colon and small intestine. Sialidases likely contribute to type F disease by enhancing CPE action and, for NanI-producing nonfoodborne human GI disease isolates, increasing intestinal growth and colonization.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Toxin gene detection and antibiotic resistance of Clostridium perfringens from aquatic sources

Clostridium perfringens is a zoonotic opportunistic pathogen that produces toxins that can cause necrotic enteritis and even "sudden death disease". This bacterium is widely distributed in the intestines of livestock and human, but there are few reports of distribution in aquatic animals (Hafeez et al., 2022). In order to explore the isolation rate of C. perfringens and the toxin genes they carry, 141 aquatic samples, including clams (Ruditapes philippinarum), oysters (Ostreidae), and mud snails (Bullacta exerata Philippi), were collected from the coastal areas of Shandong Province, China. C. perfringens strains were tested for cpa, cpb, etx, iap, cpb2, cpe, netB, and tpeL genes. 45 clam samples were boiled at 100 °C for 5 min before bacteria isolation. 80 strains were isolated from 141 samples with the positive rate being 57 %.And the positive rates of cooked clams was 87 % which was higher than the average. In detection of 8 toxin genes, all strains tested cpa positive, 3 strains netB positive, and 2 cpb and cpe, respectively. 64 strains were selected to analyze the antibiotic resistance phenotype of 10 antibiotics. The average antibiotic resistance rates of the strains to tetracycline, clindamycin, and ampicillin were 45 %, 20 %, and 16 % respectively, and the MIC of 4 strains to clindamycin was ≥128 μg/mL. A high isolation rate of C. perfringens from aquatic animals was shown, and it was isolated from boiled clams for the first time, in which cpe and netB toxin genes were detected for the first time too. The toxin encoded by cpe gene can cause food poisoning of human, thus the discoveries of this study have certain guiding significance for food safety. Antibiotics resistant C. perfringens of aquatic origin may arise from transmission in the terrestrial environment or from antibiotic contamination of the aquaculture environment and is of public health significance.

Characterization and multilocus sequence typing of Clostridium perfringens isolated from patients with diarrhoea and food poisoning in Tai'an region, China

OBJECTIVES

Clostridium perfringens (C. perfringens) is a significant opportunistic pathogen. This study aims to examine the occurrence of C. perfringens in patients with diarrhoea and food poisoning and compare the genetic similarities with strains found in poultry retail markets and poultry farms in the same city (Tai'an, China).

METHODS

Clostridium perfringens was isolated from 30 human faecal samples and genotyped using multiplex PCR. The antimicrobial susceptibility test was conducted using the Kirby-Bauer disk diffusion method. Genetic relationships were analysed through Multi-locus sequence typing (MLST) and Phylogenetic analysis.

RESULTS

The positive rate of C. perfringens was found to be 96.67%. Among the positive samples, 91.67% of the faecal samples from patients with food poisoning contained type F strains of C. perfringens, while only 16.67% of the samples from diarrhoea cases contained type F. The drug susceptibility test revealed that the majority of isolates displayed broad-spectrum antimicrobial resistance. Out of the 57 isolates tested for drug susceptibility, 89.47% demonstrated resistance to at least three antibiotics. The MLST results indicated that strains originating from the same host and environment tended to be more closely related. However, certain strains associated with food poisoning and diarrhoea in patients shared the same ST and CC as some strains found in the retail market. These strains were also found to be phylogenetically similar to some retail market strains, suggesting potential risks to human health.

CONCLUSIONS

Therefore, it is crucial to enhance the management of poultry retail markets in order to mitigate these associated risks.

A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish

Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.

Prevalence of cpe-positive Clostridium perfringens in surface-attached soil of commercially available potatoes and its significance as a potential source of food poisoning

OBJECTIVE

We aimed to examine the surface-attached soil of commercially available potatoes in Japan to determine the association between foodborne infection and the circulation of Clostridium perfringens through vegetables, soil, and environments.

METHODS

C. perfringens spores were isolated from 30 surface-attached soil samples of potatoes obtained from six regions in Japan. We performed multiplex polymerase chain reaction (PCR) and sequencing to detect the presence of six toxin and plasmid-related genes in the isolates.

RESULTS

Sulfite-reducing clostridial spores were detected in 28 (93%) of 30 potato samples, and toxin gene PCR was performed using 613 isolates. The C. perfringens α toxin gene (cpa) was detected in 288 isolates (288/613; 47%) from 25 potato samples (83%), and these isolates were presumed to be the strains of C. perfringens. The toxin types of C. perfringens were classified into type A, in which 73% of isolates had only cpa, followed by type F in 20%, type C in 6%, and type E in 0.003% (1 isolate). The enterotoxin gene (cpe) related to food poisoning was detected in 64 isolates from 9 potato samples (3%). Of these, 59 isolates had cpa and cpe, whereas five had cpa, C. perfringens β toxin gene, and cpe. All tested cpe-positive isolates had plasmid-type cpe.

CONCLUSIONS

The isolation of culturable cpe-positive C. perfringens from the surface-attached soil of commercially available potatoes indicates that potatoes are a potential source of foodborne transmission of C. perfringens.

Prevalence and Genetic Diversity of Clostridium perfringens Isolates in Hospitalized Diarrheal Patients from Central China

Objective

This study aimed to investigate the prevalence, genetic diversity and clinical characteristics of Clostridium perfringens isolates from hospitalized clinical diarrheal patients.

Methods

A prospective study was conducted on 1108 patients with diarrhea during hospitalization. Stool samples were cultured for C. perfringens, and the toxin genes were detected by PCR. The available clinical data of 112 patients were analyzed to study the clinical features of various isolates. Multi-locus sequence typing (MLST) was performed to assess phylogenetic relationship between different isolates.

Results

A total of 153 (13.8%) isolates were obtained from patients’ stools. C. perfringens type F (49.0%) was the major toxin type in the isolates, followed by type A (n = 59, 38.6%) and type C (n = 14, 9.2%). Patients older than 50 years and those with underlying diseases of cancer, hepatobiliary system, and ulcerative colitis (UC) were more predisposed to C. perfringens type F and type A infection than to type C. The patients infected with type C experienced more severe clinical symptoms compared to those with type A infection. There was a significant association between type F^C and foodborne gastrointestinal (GI) diseases (p = 0.018), between type F^P and antibiotic-associated diarrhea (AAD) (p < 0.001), and between type A and sporadic diarrhea (SD) (p < 0.001). Phylogenetic analysis indicated that type F isolates carrying a chromosomal cpe gene mainly belonged to ST77 (6/15 isolates). Type F isolates with cpe gene on a plasmid exhibited high genetic diversity.

Conclusion

High prevalence and considerable genetic diversity of C. perfringens type F were found in clinical diarrheal patients. Elderly people and patients with cancer, hepatobiliary diseases or UC, or suspected of having food poisoning (FP) may be targeted for routine testing of C. perfringens toxin genes and may benefit from early detection of C. perfringens type C isolates that cause more severe clinical symptoms.

Clonal diversity of Clostridium perfringens human clinical isolates with various toxin gene profiles based on multilocus sequence typing and alpha-toxin (PLC) typing

OBJECTIVES

Clostridium perfringens is a common anaerobic pathogen causing enteritis/enterocolitis and wound infections in humans. We analyzed clonal diversity and toxin gene prevalence in C. perfringens clinical isolates from humans in northern Japan.

METHODS

Prevalence of nine toxin genes was analyzed for 585 C. perfringens isolates from patients collected for 20-month period between May 2019 and December 2020 by molecular methods. Sequence type (ST) based on multilocus sequence typing (Xiao's scheme) and alpha-toxin (PLC) sequence type were determined for a total of 124 isolates selected in the present study along with those in our previous study (2017-2018).

RESULTS

Toxinotypes A (68.2%) was the most frequent, followed by F (31.6%), and G (0.2%), while additional toxin genes encoding binary enterotoxin (BEC/CPILE) and beta2 toxin were identified in one and six isolates, respectively. Among the 124 isolates with various toxin gene profiles, 62 STs including 53 novel types were identified, revealing the presence of six clonal complexes (CCs) consisting of 27 STs. Most of enterotoxin gene (cpe)-positive isolates belonged to CC36, CC41, and CC117. Based on 22 key amino acids in alpha toxin sequence, four PLC types (I-IV) including 21 subtypes were classified, and their relation to individual STs/CCs was clarified. Two isolates harboring bec/cpile belonged to different STs (ST95, ST131) and PLC types (If, IVb), indicating distribution of this toxin gene to distinct lineages.

CONCLUSIONS

The present study revealed the diversity in C. perfringens clones of human origin with various toxin gene profiles represented by ST/CC and PLC type.

Isolation of Alpha-Toxin-Deficient Clostridium perfringens Type F from Sewage Influents and Effluents

Clostridium perfringens is classified into types A to G, and all types produce alpha-toxins; however, C. perfringens type F that is negative for phospholipase C (PLC) activity of alpha-toxin has been isolated from the environment and cases of humans afflicted by food poisoning. This study aimed to elucidate the distribution of PLC-negative C. perfringens type F in sewage influents and effluents. Influents and effluents of two wastewater treatment plants were collected monthly between July 2016 and January 2020 and between August 2018 and January 2020, respectively. Isolation rates of PLC-negative C. perfringens type F from sewage influents and effluents were 38% (33/86) and 22% (8/36), and the numbers of isolates were 43 and 13, respectively. The locus of the enterotoxin gene of all isolates was determined to be in a plasmid with an IS1151 sequence, and multilocus sequence typing revealed that all 17 representative isolates were assigned as sequence type 186. Sequencing of the plc gene of these representative isolates showed that nonsense mutation (p.W98*) causing alpha-toxin deficiency should be responsible for a loss of PLC enzymatic activity. These results suggest that alpha toxin-deficient C. perfringens type F is distributed in living and water environments since sewage influents contain community wastewater, and effluents contaminate the environment. Detection of C. perfringens type F, independent of PLC activity, should be carried out on human and environmental samples. IMPORTANCE Understanding the diversity of biochemical characteristics that may affect the identification of bacteria is essential. C. perfringens is a ubiquitous bacterium found in the environment, humans, and animals and is responsible for infectious disease in the intestine. Although the alpha-toxin of C. perfringens may be used for its detection, variants of the alpha-toxin lacking its activity have been isolated from soil and humans experiencing symptoms of diarrhea. It is valuable to disclose the prevalence of the alpha-toxin variant in the sewage of wastewater treatment plants, as it may reflect the hygienic condition of the community, as it would be a pollution source for the environment. This study shows the persistent existence and genetic characteristics of the alpha-toxin variant in sewage and reveals a lacking mechanism of the alpha-toxin activity and proposes the detection method of C. perfringens, independent of the alpha-toxin activity.